Cannot run Metapro - errors with config.ini

[tmattes8]

Hi there, I'm having similar problems getting the pipeline to run as previously reported by a different user (issue #14 with the config.ini file). It seems like the config.ini file is being ignored, even though the pipeline output indicates the correct file (with the correct path) is being used. I replaced the default path (/project/j/jparkin/Lab_Databases) with mine (/Shared/lss_tmattes/Metapro) to no avail.

I read about using absolute paths to the config file (which I've done), and include commands to bind directories so the container knows where to look for libraries that are downloaded locally. But the output (shown below) suggests the config.ini file is not being read correctly and the python script defaults to directories from the ParkinsonLab computer, which of course won't work.

A different user figured out how to fix essentially the same problem (issue #14), but it was not detailed in the resolved issue just how the problem was fixed. Please let me know if you have some ideas on how to make the pipeline work for me.

The command string used is shown below, as is the erroneous pipeline output, which quits after trying to read the config file.

commands used: $ apptainer exec -B /Users/tmattes -B /Shared/lss_tmattes /Shared/lss_tmattes/Metapro/metapro_latest.sif python3 /pipeline/MetaPro.py -c /Shared/lss_tmattes/Metapro/config.ini -1 /Shared/lss_tmattes/34412_S1_L001_R1_001.fastq -2 /Shared/lss_tmattes/34412_S1_L001_R2_001.fastq --verbose_mode leave -o /Shared/lss_tmattes

pipeline output:

METAPRO metatranscriptomic analysis pipeline

no-host: False verbose_mode: leave working in tutorial mode: quality CHECKING CONFIG USING CONFIG /Shared/lss_tmattes/Metapro/config.ini Settings no section found, using default: genus Settings no section found, using default: 30 Settings no section found, using default: No Settings no section found, using default: bypass_log.txt Settings no section found, using default: none Settings no section found, using default: 80 Settings no section found, using default: 0.1 Settings no section found, using default: chocophlan Settings no section found, using default: 0.01 Settings no section found, using default: 90 Settings no section found, using default: 85 Settings no section found, using default: 0.65 Settings no section found, using default: 60 Settings no section found, using default: 85 Settings no section found, using default: 0.65 Settings no section found, using default: 60 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 10 Settings no section found, using default: 50 Settings no section found, using default: 10 Settings no section found, using default: 50 Settings no section found, using default: 50 Settings no section found, using default: 50 Settings no section found, using default: 50 Settings no section found, using default: 50 Settings no section found, using default: 50 Settings no section found, using default: 50 Settings no section found, using default: 5 Settings no section found, using default: 50 Settings no section found, using default: 50 Settings no section found, using default: 5 Settings no section found, using default: 60 Settings no section found, using default: 60 Settings no section found, using default: 60 Settings no section found, using default: 60 Settings no section found, using default: 1000 Settings no section found, using default: 1000 Settings no section found, using default: 60 Settings no section found, using default: 60 Settings no section found, using default: 60 Settings no section found, using default: 60 Settings no section found, using default: 60 Settings no section found, using default: 1 Settings no section found, using default: 60 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 5 Settings no section found, using default: 10 Settings no section found, using default: 1 Settings no section found, using default: yes Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: no Settings no section found, using default: high Settings no section found, using default: 25000 Settings no section found, using default: 50000 Settings no section found, using default: 50000 Labels no section found, using default: quality_filter Labels no section found, using default: host_filter Labels no section found, using default: vector_filter Labels no section found, using default: rRNA_filter Labels no section found, using default: rRNA_filter_split Labels no section found, using default: rRNA_filter_convert Labels no section found, using default: rRNA_filter_barrnap Labels no section found, using default: rRNA_filter_barrnap_merge Labels no section found, using default: rRNA_filter_barrnap_pp Labels no section found, using default: rRNA_filter_infernal Labels no section found, using default: rRNA_filter_infernal_prep Labels no section found, using default: rRNA_filter_splitter Labels no section found, using default: rRNA_filter_post Labels no section found, using default: duplicate_repopulation Labels no section found, using default: assemble_contigs Labels no section found, using default: destroy_contigs Labels no section found, using default: GA_pre_scan Labels no section found, using default: GA_split Labels no section found, using default: GA_BWA Labels no section found, using default: GA_BWA_pp Labels no section found, using default: GA_BWA_merge Labels no section found, using default: GA_BLAT Labels no section found, using default: GA_BLAT_cleanup Labels no section found, using default: GA_BLAT_cat Labels no section found, using default: GA_BLAT_pp Labels no section found, using default: GA_BLAT_merge Labels no section found, using default: GA_DMD Labels no section found, using default: GA_DMD_pp Labels no section found, using default: GA_final_merge Labels no section found, using default: taxonomic_annotation Labels no section found, using default: enzyme_annotation Labels no section found, using default: enzyme_annotation_detect Labels no section found, using default: enzyme_annotation_priam Labels no section found, using default: enzyme_annotation_priam_split Labels no section found, using default: enzyme_annotation_priam_cat Labels no section found, using default: enzyme_annotation_DMD Labels no section found, using default: enzyme_annotation_pp Labels no section found, using default: outputs Labels no section found, using default: output_copy_gene_map Labels no section found, using default: output_clean_ec Labels no section found, using default: output_copy_taxa Labels no section found, using default: output_network_generation Labels no section found, using default: output_unique_hosts_singletons Labels no section found, using default: output_unique_hosts_pair_1 Labels no section found, using default: output_unique_hosts_pair_2 Labels no section found, using default: output_unique_vectors_singletons Labels no section found, using default: output_unique_vectors_pair_1 Labels no section found, using default: output_unique_vectors_pair_2 Labels no section found, using default: output_combine_hosts Labels no section found, using default: output_per_read_scores Labels no section found, using default: output_contig_stats Labels no section found, using default: output_ec_heatmap Labels no section found, using default: output_taxa_groupby Labels no section found, using default: output_read_count Databases no section found, using default: /project/j/jparkin/Lab_Databases/univec_core/UniVec_Core.fasta Databases no section found, using default: /project/j/jparkin/Lab_Databases/Trimmomatic_adapters/TruSeq3-PE-2.fa Databases no section found, using default: /project/j/jparkin/Lab_Databases/Mouse_cds/Mouse_cds.fasta Databases no section found, using default: /project/j/jparkin/Lab_Databases/Rfam/Rfam.cm Databases no section found, using default: /project/j/jparkin/Lab_Databases/ChocoPhlAn/ChocoPhlAn.fasta Databases no section found, using default: /project/j/jparkin/Lab_Databases/family_llbs Databases no section found, using default: /project/j/jparkin/Lab_Databases/nr/nr Databases no section found, using default: /project/j/jparkin/Lab_Databases/nr/nr Databases no section found, using default: /project/j/jparkin/Lab_Databases/accession2taxid/accession2taxid Databases no section found, using default: /project/j/jparkin/Lab_Databases/WEVOTE_db/nodes.dmp Databases no section found, using default: /project/j/jparkin/Lab_Databases/WEVOTE_db/names.dmp Databases no section found, using default: /project/j/jparkin/Lab_Databases/kaiju_db/kaiju_db_nr.fmi Databases no section found, using default: /project/j/jparkin/Lab_Databases/centrifuge_db/nt Databases no section found, using default: /project/j/jparkin/Lab_Databases/swiss_prot_db/swiss_prot_db Databases no section found, using default: /project/j/jparkin/Lab_Databases/swiss_prot_db/SwissProt_EC_Mapping.tsv Databases no section found, using default: /project/j/jparkin/Lab_Databases/PRIAM_db/ Databases no section found, using default: /project/j/jparkin/Lab_Databases/DETECTv2 Databases no section found, using default: /project/j/jparkin/Lab_Databases/WEVOTE_db/ Databases no section found, using default: /project/j/jparkin/Lab_Databases/EC_pathway.txt Databases no section found, using default: /pipeline/custom_databases/pathway_to_superpathway.csv Databases no section found, using default: /pipeline_tools/mgm/MetaGeneMark_v1.mod Databases no section found, using default: /pipeline/custom_databases/FREQ_EC_pairs_3_mai_2020.txt Databases no section found, using default: /pipeline/custom_databases/taxid_trees/family_tree.tsv Databases no section found, using default: /pipeline/custom_databases/kraken2_db dir name: /project/j/jparkin/Lab_Databases/nr file name: nr /project/j/jparkin/Lab_Databases/nr/nr file does not exists

[tmattes8]

I figured out and fixed the problem. Of course, this always happens just after you get frustrated, give up and then make a public post like this. Looking forward to seeing what the pipeline can do with my data!

[DGleason-680]

Can you please share what the issue was? I'm having the same problem and I know it's a simple fix but not sure what it is.

Thanks!

[yeolex]

I figured out and fixed the problem. Of course, this always happens just after you get frustrated, give up and then make a public post like this. Looking forward to seeing what the pipeline can do with my data!

Hi, can you please comment on how you solved this issue? I appreciate your time.